1 Regress out gene signature

As we have now the gene signature for each cell type, we seek to correct for the observed bias to meet two objectives:

  1. Remove technical artifacts. We will visualize this as an increased ‘mixedness’ of “affected” and “unaffected” clusters.
  2. Preserve biological variability. Our purpose is that the only HVG that get lost are the ones present in the meta-signature.

To achieve that, we will regress out the time-score variable we computed for each cell in previous notebooks only for the genes in the meta-signatures. We will plot the tSNEs (with the HVG) before and after the correction to assess the overall performance.

This procedure is inspired by the correction of the cell cycle variability carried out in previous studies. We refer the reader to the following articles and Seurat vignette for a full understanding:

library(SingleCellExperiment)
library(scater)
library(scran)
library(Seurat)
library(EnsDb.Hsapiens.v86)
library(ggpubr)
library(org.Hs.eg.db)
library(biomaRt)
library(SC3)
library(pheatmap)
library(BiocStyle)
library(purrr)
library(ggrepel)
library(plotROC)
library(caret)
library(ROCR)
library(pheatmap)
library(org.Hs.eg.db)
library(GOstats)
library(VennDiagram)
library(ggplotify)
library(scales)
library(ggridges)
library(tidyverse)

source("bin/utils.R")

# Load SingleCellExperiment object
sce_10x <- readRDS("results/R_objects/sce_10x_scored.rds")

# Load list with metasignatures
metasignatures <- readRDS("results/R_objects/metasignatures.rds")

# Plot PCA all cells colored by label ("affected" or "unaffected")
cell_types <- c("CD4 T", "CD8 T", "NK", "Monocyte", "B")
seurat_10x <- Convert(from = sce_10x, to = "seurat")
seurat_10x <- SetAllIdent(seurat_10x, id = "cell_type")
seurat_list <- list(
  "CD4 T" = list(), 
  "CD8 T" = list(), 
  "NK" = list(), 
  "Monocyte" = list(), 
  "B" = list()
)
tsne_list <- seurat_list

for (cell_type in cell_types) {
  seurat_sub <- SubsetData(seurat_10x, ident.use = cell_type)
  for (i in c("not regressed", "regressed")) {
    seurat_curr <- ScaleData(seurat_sub, display.progress = FALSE)
    if (i == "regressed") {
      scaled_data_all <- seurat_curr@scale.data
      seurat_curr <- ScaleData(
        seurat_curr,
        genes.use = metasignatures[[cell_type]],
        vars.to.regress = "time_score",
        display.progress = FALSE
      )
      scaled_data_all[rownames(seurat_curr@scale.data), ] <- seurat_curr@scale.data
      seurat_curr@scale.data <- scaled_data_all
    } 
    seurat_curr <- FindVariableGenes(
      seurat_curr, 
      do.plot = FALSE, 
      display.progress = FALSE, 
      binning.method = "equal_frequency"
    )
    seurat_curr <- SetAllIdent(seurat_curr, id = "label")
    seurat_curr <- RunPCA(
      seurat_curr, 
      pc.genes = seurat_curr@var.genes
    )
    seurat_curr <- RunTSNE(seurat_curr)
    tsne_list[[cell_type]][[i]] <- TSNEPlot(seurat_curr)
    seurat_list[[cell_type]][[i]] <- seurat_curr
  }
}
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "RPS6"   "RPL32"  "RPS12"  "RPS3A"  "RPL21"  "RPLP2"  "RPL13"  "RPL9"   "RPS14"  "RPL31"  "RPS15A" "RPS23"  "RPS13"  "RPS27A" "RPL34"  "RPL39"  "RPS25"  "RPS8"   "RPL30"  "RPL11"  "RPL35A" "RPS28"  "RPS27"  "RPL19"  "RPL7"   "RPL10"  "RPL3"   "RPS16"  "RPL18A" "RPL13A"
## [1] ""
##  [1] "B2M"       "S100A4"    "ACTB"      "TMSB4X"    "IL32"      "HLA-A"     "CD52"      "MT-CO1"    "HLA-B"     "ANXA2"     "CRIP1"     "GZMA"      "GZMK"      "LTB"       "JUNB"      "TMSB10"    "LINC00152" "CCL5"      "HLA-DPA1"  "HOPX"      "HLA-DPB1"  "KLRB1"     "UCP2"      "LPAR6"     "LGALS3"    "CST7"      "TNFSF10"   "PRDM1"     "MT-CO2"    "ISG15"    
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "FTH1"        "EIF1"        "RPS29"       "H3F3B"       "MALAT1"      "CREM"        "EZR"         "ZNF331"      "RPS27"       "GABARAPL1"   "HERPUD1"     "BTG3"        "PMAIP1"      "RP11-51J9.5" "PIK3R1"      "ZFP36"       "H1FX"        "SYTL3"       "TSPYL2"      "FAM177A1"    "REL"         "EEF1A1"      "RGS1"        "YWHAH"       "JUND"        "DUSP2"       "RGS2"        "SLC2A3"      "RPL3"        "RBPJ"       
## [1] ""
##  [1] "TMSB10"   "CD52"     "TMSB4X"   "IL32"     "B2M"      "ACTB"     "LTB"      "RPL41"    "MT-CO1"   "RPS12"    "MT-ND4"   "RPS8"     "S100A4"   "UCP2"     "RPS3A"    "RPS25"    "RPL13"    "MT-ATP6"  "RPLP2"    "RPL19"    "MT-CYB"   "RPL32"    "MT-CO2"   "RPL28"    "RPS14"    "C1orf162" "RPS23"    "RPS26"    "RPL11"    "RPLP1"   
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "MALAT1"  "XIST"    "RPS29"   "RPS27"   "MT-CO3"  "MT-CO1"  "RPS4X"   "RPL34"   "TMSB10"  "RPL21"   "MT-ND3"  "RPL7"    "RPS18"   "TMSB4X"  "LDLRAP1" "NUCB2"   "AIF1"    "STMN1"   "RPL3"    "RPL31"   "RPL39"   "MT-ND4"  "HLA-B"   "FAIM3"   "RPS28"   "MT-CYB"  "ID3"     "TAGAP"   "ANKRD44" "RPS14"  
## [1] ""
##  [1] "RPS26"    "KLRB1"    "RPL28"    "RPS16"    "RPLP1"    "FTH1"     "RPS12"    "RPL10"    "GNLY"     "IL32"     "S100A4"   "CREM"     "RPS19"    "TNFRSF4"  "RPL13A"   "FAM177A1" "LGALS3"   "RPS8"     "JUNB"     "EIF1"     "RPL27A"   "HOPX"     "RPL18A"   "ATG2A"    "ANXA2"    "RPL13"    "ZNF331"   "B4GALT1"  "PIK3R1"   "CNOT6L"  
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "MT-ND2"  "MT-CYB"  "MT-CO2"  "MT-ND4"  "MT-ATP6" "CCL5"    "MT-CO3"  "MT-ND3"  "GZMK"    "MT-CO1"  "NKG7"    "RPL27A"  "GZMA"    "CST7"    "RPS19"   "CD8B"    "FTH1"    "DUSP2"   "GNLY"    "RPL23A"  "RPL41"   "CD8A"    "RPL13A"  "RPS27A"  "RPLP2"   "B2M"     "RPL34"   "RPS16"   "RPLP1"   "RPS3"   
## [1] ""
##  [1] "TSHZ2"        "TMSB10"       "IL6ST"        "ID3"          "FHIT"         "C1orf162"     "STMN1"        "MARCKSL1"     "LTB"          "LPAR6"        "CD52"         "UCP2"         "PIM2"         "HLA-DRA"      "FAIM3"        "LDLRAP1"      "RPS13"        "RP11-51J9.5"  "BIRC3"        "LIMS1"        "H1FX"         "ACTB"         "ISG15"        "YIPF4"        "XIST"         "MAPKAPK5-AS1" "FXR1"         "RBCK1"        "KAT6A"        "OTUB1"       
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "MT-ATP6"  "RPS26"    "CD8B"     "MT-CO2"   "MT-ND2"   "AIF1"     "MT-ND4"   "MT-CYB"   "CD8A"     "FHIT"     "MALAT1"   "MT-ND3"   "HLA-DPB1" "APBA2"    "MT-CO3"   "RGS1"     "CMC1"     "NKG7"     "RPLP2"    "ANKRD44"  "OGT"      "RPL28"    "NUCB2"    "RPS16"    "CCL5"     "JUND"     "HLA-DPA1" "TTC14"    "MDM4"     "CST7"    
## [1] ""
##  [1] "LTB"     "RPS4X"   "KLRB1"   "EEF1A1"  "RPS18"   "S100A4"  "RPL3"    "RPS2"    "RPL10"   "JUNB"    "RPL41"   "TNFRSF4" "HLA-B"   "B2M"     "CRIP1"   "RPL18A"  "RPL34"   "HOPX"    "RPL39"   "ANXA2"   "HLA-A"   "ACTB"    "CD52"    "RPL21"   "RPL23A"  "RPS29"   "RPS3"    "RPL13A"  "LGALS3"  "FTH1"   
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "RPL32"  "RPS3A"  "RPS12"  "RPS6"   "RPL13"  "RPLP2"  "RPS14"  "RPS23"  "RPL21"  "RPS15A" "RPS13"  "RPL31"  "RPS27A" "RPS8"   "RPS25"  "RPL19"  "RPL11"  "RPL34"  "RPL35A" "RPL30"  "RPL9"   "RPS28"  "RPL10"  "RPL7"   "RPL18A" "RPL13A" "RPL39"  "RPLP1"  "RPL27A" "RPS19" 
## [1] ""
##  [1] "FTH1"      "HLA-B"     "S100A4"    "HLA-A"     "EIF1"      "ANXA2"     "B2M"       "JUNB"      "LINC00152" "GZMK"      "CCL5"      "CREM"      "EZR"       "KLRB1"     "HLA-DPA1"  "HLA-DPB1"  "ACTB"      "HOPX"      "GZMA"      "CST7"      "H3F3B"     "LGALS3"    "IL32"      "HERPUD1"   "PRDM1"     "PIK3R1"    "CRIP1"     "GATA3"     "RGS1"      "NKG7"     
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "MALAT1"  "RPS29"   "RPS27"   "XIST"    "RPS4X"   "MT-CO3"  "RPL34"   "RPL21"   "MT-CO1"  "RPS18"   "RPL3"    "RPL7"    "RPL39"   "H3F3B"   "MT-ND3"  "ID3"     "H1FX"    "HLA-B"   "RPL31"   "RPS28"   "LDLRAP1" "NUCB2"   "EEF1A1"  "STMN1"   "AIF1"    "FAIM3"   "TMSB4X"  "KTN1"    "TAGAP"   "TMSB10" 
## [1] ""
##  [1] "RPS26"    "IL32"     "RPL28"    "KLRB1"    "RPS16"    "RPLP1"    "S100A4"   "RPS12"    "GNLY"     "RPL10"    "RPS19"    "TNFRSF4"  "RPS8"     "RPL13A"   "RPL27A"   "CD52"     "RPL13"    "GZMA"     "LGALS3"   "HOPX"     "CREM"     "RPL19"    "MT-ND2"   "RPL18A"   "ANXA2"    "FTH1"     "RPL41"    "RPS15"    "FAM177A1" "JUNB"    
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "TSHZ2"        "FHIT"         "IL6ST"        "STMN1"        "C1orf162"     "ID3"          "MARCKSL1"     "TMSB10"       "HLA-DRA"      "PIM2"         "ISG15"        "UCP2"         "RP11-51J9.5"  "FAIM3"        "LDLRAP1"      "LIMS1"        "LTB"          "YIPF4"        "LPAR6"        "CD52"         "BIRC3"        "RBCK1"        "FXR1"         "MAPKAPK5-AS1" "RPS13"        "KAT6A"        "OTUB1"        "OXNAD1"       "STAT1"        "H1FX"        
## [1] ""
##  [1] "MT-ND2"  "MT-CYB"  "MT-ND4"  "MT-CO2"  "MT-CO3"  "MT-ATP6" "CCL5"    "MT-CO1"  "MT-ND3"  "B2M"     "GZMK"    "RPL27A"  "GZMA"    "RPL41"   "NKG7"    "RPL34"   "RPS19"   "FTH1"    "CST7"    "RPS27A"  "RPL23A"  "DUSP2"   "CD8B"    "RPS15A"  "RPL13A"  "HLA-A"   "IL32"    "RPLP2"   "RPL10"   "RPS3"   
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "EEF1A1"  "FTH1"    "RPL3"    "KLRB1"   "RPS4X"   "S100A4"  "RPS2"    "RPL10"   "RPS18"   "LTB"     "EIF1"    "JUNB"    "RPS29"   "RPL21"   "RPL34"   "ZFP36"   "BTG3"    "HERPUD1" "YWHAH"   "TNFRSF4" "RPL18A"  "HLA-A"   "CRIP1"   "RPS27"   "CREM"    "SYTL3"   "H3F3B"   "SLC2A3"  "RPL39"   "REL"    
## [1] ""
##  [1] "MT-ATP6"  "MT-CO2"   "MT-CYB"   "MT-ND4"   "MT-ND2"   "CD8B"     "TMSB10"   "AIF1"     "MT-ND3"   "MT-CO1"   "FHIT"     "ANKRD44"  "RPS26"    "STMN1"    "TTC14"    "MT-CO3"   "NUCB2"    "FAIM3"    "IFI6"     "HLA-DPB1" "CD8A"     "MTRNR2L8" "LDLRAP1"  "OXNAD1"   "OGT"      "GPR155"   "GZMK"     "HLA-DPA1" "ASCC2"    "MIR142"  
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "TMSB10"       "B2M"          "TMSB4X"       "PTMA"         "H3F3B"        "ACTB"         "RPS15A"       "SESN3"        "RGS1"         "AP3M2"        "FTH1"         "CD52"         "LPAR6"        "NR3C1"        "RPL41"        "FAM177A1"     "RPL11"        "BIRC3"        "MT-ATP6"      "MT-CYB"       "EIF1"         "MT-ND4"       "SLC2A3"       "RPL28"        "MT-CO2"       "RP11-51J9.5"  "JUND"         "DNAJB1"       "PIK3R1"       "RP11-138A9.2"
## [1] ""
##  [1] "GZMK"       "CCL5"       "NKG7"       "GZMA"       "GNLY"       "HOPX"       "CST7"       "RPS2"       "CD8A"       "RPS29"      "CMC1"       "AC092580.4" "CD8B"       "RPL3"       "EEF1A1"     "KLRB1"      "DUSP2"      "LGALS3"     "CASP1"      "EHD1"       "NUCB2"      "RPS19"      "RPS4X"      "RPS18"      "RPS27"      "RPL31"      "HLA-B"      "PSMA5"      "MT-ND3"     "RPS3"      
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "B2M"      "PFN1"     "ACTB"     "TMSB4X"   "IL32"     "CD52"     "TMSB10"   "S100A4"   "MT-CO1"   "NKG7"     "GZMH"     "CCL5"     "HLA-A"    "GZMK"     "HLA-C"    "FAM65B"   "CD8B"     "HLA-DRB1" "HOPX"     "SELL"     "KLRF1"    "LGALS1"   "CMC1"     "COTL1"    "HLA-DRA"  "FERMT3"   "DDX17"    "FCGR3A"   "STMN1"    "MT1E"    
## [1] ""
##  [1] "FTH1"         "EIF1"         "RPL10"        "RPL34"        "RPL21"        "EEF1A1"       "RPS27"        "H3F3B"        "TSPYL2"       "RPS12"        "RPS6"         "RPL32"        "RPL39"        "FOS"          "RPS27A"       "JUN"          "RP11-277L2.4" "JUND"         "PTMA"         "PMAIP1"       "RPS29"        "CNOT1"        "RPL7"         "KLRB1"        "SKIL"         "H1FX"         "RGCC"         "RPS2"         "SYTL3"        "RPS19"       
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "MALAT1"  "H3F3B"   "HLA-B"   "NEAT1"   "HLA-C"   "EIF1"    "MT-CO3"  "H1FX"    "CLK1"    "PTPN7"   "NKG7"    "HLA-A"   "CNOT1"   "ZNF281"  "ZEB2"    "CCNH"    "SPON2"   "SAMSN1"  "ZBTB7A"  "DDIT3"   "MT-CO2"  "RASA2"   "PICALM"  "SP140L"  "LAMTOR3" "SMG1"    "BBC3"    "HAUS3"   "GMFB"    "ARMCX3" 
## [1] ""
##  [1] "RPL13"  "RPS12"  "RPL32"  "LTB"    "RPS6"   "RPL10"  "RPS18"  "IL32"   "CD52"   "RPS14"  "RPS2"   "RPL13A" "GZMK"   "RPLP1"  "RPL21"  "RPS27A" "S100A4" "EEF1A1" "KLRB1"  "RPS19"  "RPL41"  "AQP3"   "RPLP2"  "RPL7"   "RPL34"  "ACTB"   "RPL39"  "LST1"   "LGALS3" "RPS15A"
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "GNLY"     "TYROBP"   "NKG7"     "MT-CO2"   "SPON2"    "KLRF1"    "MT-ND4"   "MT-ATP6"  "FCER1G"   "KLRB1"    "C20orf24" "PTGDS"    "MT-ND2"   "CLIC3"    "RPL10"    "THEMIS2"  "FCGR3A"   "SYTL3"    "RPLP1"    "IFNGR1"   "NEIL1"    "MT-CYB"   "F2R"      "KLRC1"    "RIN3"     "C1orf162" "CCL3"     "YES1"     "MT-ND3"   "GZMH"    
## [1] ""
##  [1] "XIST"     "GPR183"   "GZMK"     "COTL1"    "LTB"      "RGS1"     "CD52"     "JUN"      "SAMSN1"   "HLA-DRB1" "RPS29"    "RPS18"    "ASF1A"    "RPL39"    "IL32"     "RPS27"    "PLK3"     "H1FX"     "NABP1"    "ACTB"     "ARMCX3"   "TMBIM6"   "GPR82"    "HSPB1"    "RPS2"     "SMARCC1"  "NIN"      "NFKBIZ"   "CD8B"     "CCDC66"  
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "KLRB1"        "GNLY"         "TYROBP"       "MT-ND2"       "ACAA2"        "MT-ND4"       "MT-CO2"       "MT-CYB"       "MT-ATP6"      "ARHGAP5"      "S100A4"       "FCER1G"       "PDE7A"        "KLRF1"        "RP11-83A24.2" "NAA16"        "S100A9"       "TATDN1"       "ADSS"         "C1orf162"     "NXT1"         "FNTA"         "HOPX"         "PTMA"         "BMS1"         "CERS5"        "GPR82"        "RASA2"        "DMTF1"        "C15orf61"    
## [1] ""
##  [1] "RPS29"    "HLA-DRB1" "MALAT1"   "RPS27"    "CD8A"     "CD8B"     "CCL5"     "COTL1"    "RPL13A"   "RPS18"    "HLA-B"    "GZMH"     "ZEB2"     "HLA-DRA"  "RANBP2"   "SPPL2A"   "PSMA6"    "CENPC"    "ARL6IP1"  "TIPARP"   "KIAA1551" "HLA-C"    "MED15"    "RAB8B"    "CLIP1"    "CMC1"     "NELFE"    "RFC1"     "PRPF18"   "ERICH1"  
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "RPS27"    "MALAT1"   "NKG7"     "CMC1"     "CCL5"     "RPL21"    "GZMH"     "RPS29"    "RPS14"    "RPS27A"   "RPS19"    "RPL39"    "RPS15A"   "CD8B"     "RPL41"    "RPL13A"   "HLA-B"    "TMSB4X"   "CEP78"    "HLA-DRB1" "RPLP2"    "HLA-C"    "EOMES"    "CD8A"     "RPL7"     "CCL3"     "GNPTAB"   "F2R"      "B2M"      "HLA-A"   
## [1] ""
##  [1] "KLRB1"        "LTB"          "AQP3"         "BCL7C"        "H2AFX"        "PTMA"         "USP36"        "S100A4"       "PRKDC"        "DBF4"         "RNF138"       "RAB8B"        "UBE2D1"       "TIPARP"       "RP11-356I2.4" "NELFE"        "DENR"         "RANBP2"       "IL4R"         "PTBP3"        "IQGAP2"       "ZNF224"       "MYO9B"        "RFC1"         "KXD1"         "SIRT2"        "RPL7L1"       "PRPF18"       "LMAN1"        "CMIP"        
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "MALAT1"        "NKG7"          "HLA-C"         "B2M"           "HLA-A"         "HLA-B"         "GZMH"          "MT-CO1"        "H3F3B"         "MT-CO2"        "TMSB10"        "SPON2"         "TMSB4X"        "LGALS1"        "TYROBP"        "PFN1"          "KLRF1"         "GNLY"          "MT-ATP6"       "ZEB2"          "NEAT1"         "HLA-DRB1"      "MT-CO3"        "PTPN7"         "ZBTB7A"        "FCER1G"        "FCGR3A"        "C20orf24"      "CMC1"          "RP11-139H15.1"
## [1] ""
##  [1] "RPL13"  "RPS12"  "RPL32"  "RPL10"  "RPS6"   "RPL21"  "LTB"    "EEF1A1" "RPS2"   "RPS18"  "RPL13A" "RPS14"  "RPS27A" "RPLP1"  "KLRB1"  "RPL34"  "RPS19"  "GZMK"   "RPL7"   "RPLP2"  "RPL39"  "AQP3"   "RPL41"  "IL32"   "CD52"   "RPS15A" "S100A4" "LST1"   "RPS27"  "FOS"   
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "JUN"          "RPS27"        "H1FX"         "RPS29"        "XIST"         "RGS1"         "SAMSN1"       "RP11-277L2.4" "PLK3"         "RPL39"        "GPR183"       "CD69"         "RPL34"        "ARMCX3"       "GCC2"         "LTB"          "FOS"          "BTG2"         "NFKBIZ"       "RGCC"         "CLK1"         "NXT1"         "SKIL"         "LMNA"         "H3F3B"        "GZMK"         "HAUS3"        "DNAJB1"       "ASF1A"        "CCNH"        
## [1] ""
##  [1] "GNLY"     "NKG7"     "TYROBP"   "KLRF1"    "MT-CO2"   "GZMH"     "B2M"      "SPON2"    "MT-ND4"   "FCER1G"   "FCGR3A"   "C20orf24" "MT-ATP6"  "PTGDS"    "C1orf162" "RPL10"    "LAIR2"    "CLIC3"    "CMC1"     "KLRC1"    "MT-CYB"   "HLA-A"    "KLRB1"    "HLA-C"    "THEMIS2"  "RPLP1"    "LGALS1"   "S100A4"   "TXK"      "F2R"     
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "HLA-DRB1" "COTL1"    "GZMH"     "HLA-DRA"  "CD8A"     "STMN1"    "CD8B"     "LGALS1"   "TMSB10"   "CMC1"     "MT1E"     "ACTB"     "TMSB4X"   "CCL5"     "PCNA"     "RGS1"     "XIST"     "TUBB"     "HLA-A"    "ITGAL"    "CXCR3"    "MYO1G"    "GPR183"   "DDX17"    "CD52"     "IFI16"    "HIST1H4C" "PAG1"     "EIF1"     "FKBP3"   
## [1] ""
##  [1] "MT-ND2"       "KLRB1"        "MT-CO2"       "MT-ND4"       "MT-CO3"       "MT-ND3"       "MT-ATP6"      "MT-CYB"       "RPL34"        "GNLY"         "TYROBP"       "EEF1A1"       "MT-CO1"       "RPL7"         "RPL21"        "RPS6"         "CD69"         "RPS27A"       "RPLP2"        "HOPX"         "RPLP1"        "FCER1G"       "RPL32"        "RP11-277L2.4" "ARHGAP5"      "IL4R"         "YES1"         "CXXC5"        "MALAT1"       "RPS12"       
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "KLRB1"    "LTB"      "PTMA"     "S100A4"   "AQP3"     "STMN1"    "IL32"     "FTH1"     "ACTB"     "TUBB"     "H2AFX"    "PRKDC"    "HIST1H4C" "BCL7C"    "USP36"    "LGALS3"   "NELFE"    "RAB8B"    "RNF138"   "IFNGR1"   "UBE2D1"   "DENR"     "IL4R"     "IQGAP2"   "RANBP2"   "PCNA"     "DBF4"     "MYO9B"    "RFC1"     "PRPF18"  
## [1] ""
##  [1] "RPS27"  "MALAT1" "RPS29"  "RPL21"  "CCL5"   "RPS14"  "CMC1"   "NKG7"   "RPS27A" "RPL13A" "RPL39"  "CD8B"   "RPS15A" "RPL7"   "GZMH"   "RPS19"  "RPL41"  "HLA-B"  "RPL34"  "TMSB4X" "RPLP2"  "EOMES"  "B2M"    "CD8A"   "HLA-C"  "CCL3"   "CEP78"  "GNPTAB" "NEAT1"  "F2R"   
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "GNLY"          "TYROBP"        "ACAA2"         "KLRF1"         "KLRB1"         "PDE7A"         "FCER1G"        "S100A9"        "ARHGAP5"       "C1orf162"      "TATDN1"        "TUBB"          "CERS5"         "COMMD7"        "NOP56"         "RASA2"         "RP11-139H15.1" "S100A4"        "FNTA"          "C15orf61"      "SMARCC1"       "RP11-83A24.2"  "HSPB1"         "ADSS"          "NLRP1"         "USP22"         "USF2"          "NAA16"         "DMTF1"         "PTGDS"        
## [1] ""
##  [1] "RPS29"        "MALAT1"       "RPS18"        "TIPARP"       "RPS27"        "CENPC"        "SPPL2A"       "RANBP2"       "RP11-356I2.4" "PSMA6"        "RAB8B"        "DBF4"         "PTBP3"        "SH2D2A"       "RFC1"         "SIRT7"        "COPA"         "AKAP9"        "TOPORS"       "BCL7C"        "RPL13A"       "CMIP"         "ZNF224"       "H2AFX"        "CLIP1"        "YES1"         "VPS37B"       "RAB7L1"       "PRPF18"       "LMAN1"       
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "PFN1"     "ACTB"     "TMSB4X"   "GZMA"     "TMSB10"   "B2M"      "S100A4"   "FCER1G"   "NKG7"     "GZMB"     "IL32"     "CD52"     "CCL4"     "MT-CO1"   "FCRL6"    "HLA-A"    "CD320"    "CSK"      "DUT"      "TUBA1B"   "MYOM2"    "LAIR2"    "C17orf62" "MRPL34"   "CCL5"     "BATF"     "BOLA3"    "RASSF7"   "DCK"      "CD3D"    
## [1] ""
##  [1] "FTH1"        "EIF1"        "H3F3B"       "IFNGR1"      "PIK3R1"      "CNOT1"       "RPS27"       "PMAIP1"      "SLA2"        "GABARAPL1"   "TSPYL2"      "CREM"        "RPL13A"      "RGS1"        "JUN"         "EEF1A1"      "FAM177A1"    "ZNF331"      "RPL21"       "NR4A2"       "MALAT1"      "OSER1"       "RP11-51J9.5" "JUND"        "FOS"         "FAM133B"     "METRNL"      "EML4"        "RPL10"       "RPS15A"     
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "CD3D"   "CD3G"   "CD52"   "RPS12"  "CD8B"   "RPL13A" "RPS27"  "RPS19"  "IL32"   "RPS14"  "RPLP2"  "RPS15A" "CCL5"   "GZMK"   "CD8A"   "RPL10"  "RPL34"  "RPL41"  "RPL21"  "RPS18"  "RPS27A" "EEF1A1" "MT1E"   "RPLP1"  "LTB"    "RPL7"   "KLRC1"  "DDX3Y"  "XCL1"   "SELL"  
## [1] ""
##  [1] "MT-CO1"  "MALAT1"  "FCER1G"  "MT-CO3"  "GZMB"    "H3F3B"   "MT-CO2"  "HLA-C"   "HLA-B"   "B2M"     "NKG7"    "KLRB1"   "MT-ND4"  "PTMA"    "GNLY"    "HLA-A"   "XIST"    "MT-ATP6" "ACTB"    "CCL4"    "PFN1"    "EIF1"    "CCL3"    "TMSB10"  "TUBA1B"  "MT-ND3"  "DIP2A"   "TMSB4X"  "GZMA"    "AK5"    
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "EIF1"     "NKG7"     "H3F3B"    "KLRB1"    "FOS"      "RPL10"    "GZMB"     "NR4A2"    "IRF8"     "PTMA"     "RGS1"     "DUSP1"    "FCER1G"   "PMAIP1"   "TSPYL2"   "RGS2"     "JUND"     "DDIT3"    "CCL4"     "METRNL"   "ZNF331"   "JUN"      "DUSP10"   "CREM"     "PDE4D"    "RAMP1"    "HIST1H1C" "SCLT1"    "KRT86"    "FTH1"    
## [1] ""
##  [1] "AP1G1"        "USP7"         "GPM6B"        "ANKRD13D"     "CNTRL"        "TTTY15"       "LPGAT1"       "SPTAN1"       "AC084018.1"   "SUZ12"        "CEP95"        "KLF10"        "LRBA"         "RB1"          "PSTPIP2"      "CASP3"        "TP53"         "GDI1"         "FAM78A"       "FAM228B"      "VAV1"         "ZFC3H1"       "RAD51C"       "CTD-3184A7.4" "ACAT2"        "DNAJC5"       "ACYP2"        "PIKFYVE"      "CRLF3"        "IKBKG"       
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "MT-CO2"  "MT-ND2"  "MT-ATP6" "MT-ND4"  "GNLY"    "MT-CYB"  "RPL10"   "RPLP2"   "RPL41"   "KLRB1"   "RPLP1"   "RPL21"   "RPS12"   "RPS27A"  "MT-CO3"  "RPS15A"  "RPS14"   "MT-CO1"  "B2M"     "RPL34"   "MYOM2"   "PTGDS"   "MT-ND3"  "EEF1A1"  "RPL13A"  "RPL7"    "RPS19"   "KLRC1"   "NKG7"    "PTMA"   
## [1] ""
##  [1] "IFNG"        "JUN"         "RGS1"        "CD3D"        "PMAIP1"      "CCL3"        "FOS"         "CD8A"        "DUSP10"      "CD8B"        "CD3G"        "XIST"        "KLF6"        "CNOT1"       "DUSP1"       "RPS29"       "H1FX"        "PPP1R15A"    "IRF8"        "CCL4"        "TUBB"        "HIST1H1C"    "PCNA"        "LMO4"        "RP11-51J9.5" "AASDHPPT"    "JUND"        "BTG3"        "DDIT3"       "STMN1"      
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "KLRB1"        "RPLP1"        "PLEKHA2"      "MYOM2"        "TTTY15"       "AC132872.2"   "STMN1"        "TP53"         "KLF10"        "VIPR2"        "KRT86"        "PTMA"         "FCER1G"       "GON4L"        "AASDHPPT"     "KLRC1"        "LAIR2"        "RP3-477O4.14" "DDX3Y"        "GZMB"         "PTGDS"        "DNAJC5"       "NIPA2"        "CASP3"        "RB1"          "AUTS2"        "FAM177A1"     "B3GNT7"       "IFITM3"       "DENND3"      
## [1] ""
##  [1] "RPS27"  "RPS29"  "MALAT1" "CD3D"   "CD3G"   "HLA-B"  "HLA-C"  "XIST"   "RPL34"  "B2M"    "RPL41"  "MT-CO1" "CD8B"   "KLF6"   "MT-CO3" "RPL21"  "CD8A"   "CD52"   "RPS18"  "RPS14"  "RPL13A" "MITD1"  "RPL7"   "RPS27A" "EEF1A1" "TMSB4X" "CCL5"   "GZMK"   "MT-ND3" "RPS15A"
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "CD3D"   "CD52"   "CD3G"   "CD8B"   "IL32"   "RPS12"  "CCL5"   "RPS19"  "CD8A"   "GZMK"   "RPLP2"  "RPL13A" "RPS14"  "RPS27"  "RPL10"  "RPS15A" "RPL41"  "MT1E"   "RPS18"  "RPL34"  "KLRC1"  "LTB"    "RPL21"  "CD320"  "S100A4" "SELL"   "RPS27A" "RPLP1"  "EEF1A1" "DDX3Y" 
## [1] ""
##  [1] "MALAT1"  "H3F3B"   "MT-CO3"  "FCER1G"  "MT-CO1"  "MT-CO2"  "GZMB"    "HLA-B"   "KLRB1"   "FTH1"    "EIF1"    "PTMA"    "HLA-C"   "B2M"     "MT-ND4"  "NKG7"    "MT-ATP6" "CCL3"    "GNLY"    "XIST"    "DUSP1"   "IRF8"    "CCL4"    "PMAIP1"  "HLA-A"   "TSPYL2"  "CREM"    "MT-ND3"  "ACTB"    "METRNL" 
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "TUBA1B"   "GZMB"     "ACTB"     "STMN1"    "PCNA"     "DUT"      "MT-CO1"   "HLA-C"    "XIST"     "HLA-A"    "MYOM2"    "FCER1G"   "NKG7"     "MRPL34"   "CSK"      "TMSB10"   "BOLA3"    "PFN1"     "ACADM"    "AK5"      "MRPL27"   "CXCR2"    "SIGLEC7"  "RASSF7"   "MCM7"     "ANKRD36C" "GZMA"     "TRPV2"    "BATF"     "PYCR2"   
## [1] ""
##  [1] "RPS27"        "RPL21"        "RPL13A"       "RPL34"        "RPS15A"       "RPS14"        "RPS27A"       "EEF1A1"       "RPS12"        "RPL7"         "RPL41"        "RPLP2"        "RP11-51J9.5"  "RPS19"        "EML4"         "RPS29"        "RPLP1"        "RPS18"        "MT-ND2"       "NUP54"        "BIRC2"        "DENND3"       "PSME4"        "MED23"        "GPM6B"        "PER1"         "RP11-138A9.2" "C9orf89"      "PTAR1"        "CEP95"       
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "FAM78A"     "KLF10"      "CNTRL"      "VAV1"       "IKBKG"      "ACAT2"      "TP53"       "CRLF3"      "EHMT1"      "RAD51C"     "RB1"        "PSTPIP2"    "AC084018.1" "TTTY15"     "NIPA2"      "LPGAT1"     "AP1G1"      "SUZ12"      "USP7"       "SPTAN1"     "TUBB"       "FAM228B"    "CASP3"      "ANKRD13D"   "DNAJC5"     "GTF2I"      "FAM134C"    "GPM6B"      "PIKFYVE"    "LRBA"      
## [1] ""
##  [1] "RPL10"  "NKG7"   "KLRB1"  "RPL13A" "RPL41"  "EEF1A1" "EIF1"   "RPS15A" "FOS"    "RPLP1"  "RGS2"   "JUND"   "TMSB10" "RPL21"  "KRT86"  "GNLY"   "RPL34"  "PDE4D"  "DUSP1"  "IRF8"   "DDIT3"  "B2M"    "RPS12"  "DUSP10" "PER1"   "GZMB"   "PTMA"   "BTG3"   "B3GNT7" "DNAJB1"
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "JUN"          "PMAIP1"       "RGS1"         "IFNG"         "FOS"          "CCL3"         "DUSP10"       "DUSP1"        "KLF6"         "PPP1R15A"     "IRF8"         "JUND"         "HIST1H1C"     "H1FX"         "RPS29"        "CD3D"         "BTG3"         "DDIT3"        "XIST"         "H3F3B"        "CD8A"         "PHF1"         "CCL4"         "CD8B"         "CNOT1"        "CD3G"         "SKIL"         "LYST"         "RP11-277L2.4" "PIK3R1"      
## [1] ""
##  [1] "MT-CO2"  "MT-ND4"  "MT-ND2"  "MT-ATP6" "MT-CYB"  "GNLY"    "B2M"     "MT-CO1"  "RPLP2"   "MYOM2"   "MT-CO3"  "KLRB1"   "RPLP1"   "RPL10"   "RPL41"   "RPS12"   "TMSB10"  "MT-ND3"  "RPS27A"  "PTGDS"   "IL32"    "RPL21"   "S100A4"  "RPS15A"  "RPS14"   "NKG7"    "RPS19"   "RPL34"   "KLRC1"   "TMSB4X" 
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "CD3D"    "MALAT1"  "CD3G"    "B2M"     "HLA-C"   "RPS27"   "RPS29"   "HLA-B"   "CD8B"    "XIST"    "MT-CO1"  "CD8A"    "CD52"    "MT-CO3"  "PFN1"    "HLA-A"   "TMSB4X"  "MITD1"   "RPL34"   "CCL5"    "RPL41"   "ACTB"    "AK5"     "MT-ND3"  "KLF6"    "DNM1L"   "SYNGR1"  "FTX"     "BCL2L13" "RPS18"  
## [1] ""
##  [1] "KLRB1"        "FCER1G"       "RPLP1"        "PLEKHA2"      "AC132872.2"   "KLRC1"        "TTTY15"       "GZMB"         "VIPR2"        "MYOM2"        "XCL1"         "DDX3Y"        "TP53"         "IFITM3"       "AASDHPPT"     "KRT86"        "GON4L"        "CASP3"        "KLF10"        "SP140L"       "B3GNT7"       "BTG3"         "CCL3"         "COMMD5"       "AUTS2"        "RP3-477O4.14" "HAVCR2"       "SOX4"         "MEX3C"        "PDE4D"       
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "PPBP"      "HIST1H2AC" "PF4"       "CCL5"      "SDPR"      "NRGN"      "RGS18"     "GNG11"     "TUBB1"     "CLU"       "ACRBP"     "F13A1"     "RUFY1"     "MMD"       "NCOA4"     "CCND3"     "NGFRAP1"   "VCL"       "MAX"       "YWHAH"     "TLN1"      "LIMS1"     "TSC22D1"   "MAP3K7CL"  "VIM-AS1"   "ETFA"      "XPNPEP1"   "RAP1B"     "MYL12A"    "RNF11"    
## [1] ""
##  [1] "RPL34"       "RPLP1"       "G0S2"        "IL8"         "MALAT1"      "NEAT1"       "C15orf48"    "THBS1"       "PLIN2"       "FTH1"        "SDC2"        "CXCL2"       "S100A6"      "SRGN"        "EREG"        "LYZ"         "CTA-29F11.1" "GAPDH"       "PHLDA1"      "HK2"         "TIMP1"       "ADM"         "CXCL3"       "ERO1L"       "PTGES"       "HLA-DRA"     "H1F0"        "EGR1"        "ASPH"        "SNAPC1"     
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "S100A4"  "AIF1"    "ACTB"    "OAZ1"    "RPS19"   "TMSB4X"  "DYNLL1"  "ARL6IP5" "MT-CO2"  "S100A9"  "MYL12A"  "NKG7"    "GZMA"    "S100A8"  "HOPX"    "CD74"    "ISG15"   "MYL6"    "GNLY"    "KLRB1"   "GZMB"    "SPON2"   "CST7"    "MT-CO1"  "IL32"    "CD7"     "LYPD2"   "CMC1"    "SKAP2"   "PRF1"   
## [1] ""
##  [1] "FTH1"        "TIMP1"       "SRGN"        "G0S2"        "IL8"         "C15orf48"    "PLIN2"       "THBS1"       "SAT1"        "GAPDH"       "SDC2"        "RGCC"        "HK2"         "CXCL2"       "CTA-29F11.1" "CD9"         "PHLDA1"      "SMOX"        "H3F3B"       "NEAT1"       "GPX1"        "ADM"         "EREG"        "CXCL3"       "ERO1L"       "MIR4435-1HG" "ASPH"        "PTGES"       "HILPDA"      "MPP1"       
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "LYZ"           "S100A9"        "HLA-DRB1"      "GPX1"          "FCER1A"        "S100A8"        "CD74"          "HLA-DRA"       "PLBD1"         "RP11-1143G9.4" "CLEC10A"       "MFSD1"         "S100A12"       "RGS18"         "S100A6"        "S100A4"        "YWHAH"         "SDPR"          "TUBA1C"        "GSN"           "GNG11"         "PF4"           "F13A1"         "CAPN2"         "TUBB1"         "SPINT2"        "MAP3K7CL"      "AIF1"          "SNAP23"        "TMEM55A"      
## [1] ""
##  [1] "NKG7"     "GNLY"     "GZMB"     "GZMA"     "KLRB1"    "FGFBP2"   "CST7"     "CD7"      "HOPX"     "SPON2"    "PRF1"     "CCL4"     "IL32"     "CMC1"     "CCL5"     "MALAT1"   "B2M"      "JAK1"     "NEAT1"    "H3F3B"    "CCL3"     "MAP3K8"   "SAT1"     "FTH1"     "MT-CO2"   "MT-CO3"   "PLIN2"    "MT-CO1"   "RPS19"    "C15orf48"
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "HLA-DPB1" "RPS19"    "NAP1L1"   "CD74"     "HLA-DRB1" "HLA-DRA"  "LYPD2"    "C1QA"     "VMO1"     "FTH1"     "MALAT1"   "SAT1"     "RAP1B"    "FAM110A"  "MT2A"     "AIF1"     "BIN2"     "CLEC10A"  "TIMP1"    "FCER1A"   "CD47"     "ICAM2"    "NDUFA6"   "CTSL"     "MYL6"     "ARL6IP5"  "NDNL2"    "SNAP23"   "SNN"      "SPINT2"  
## [1] ""
##  [1] "S100A8"        "S100A9"        "S100A12"       "LYZ"           "RP11-1143G9.4" "GPX1"          "S100A6"        "RPLP1"         "RETN"          "CSF3R"         "PLBD1"         "PPBP"          "TMEM91"        "MT-CO3"        "F13A1"         "S100P"         "CYP1B1"        "GNLY"          "HOPX"          "GNG11"         "RPL34"         "CCL5"          "NRGN"          "GZMA"          "EGR1"          "S100A4"        "MT-CO1"        "PF4"           "RNU12"         "GZMB"         
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "FTL"      "B2M"      "AIF1"     "S100A4"   "S100A6"   "TMSB4X"   "OAZ1"     "SAT1"     "NEAT1"    "MT-CO1"   "MALAT1"   "ITM2B"    "MT-CO2"   "ACTB"     "LYPD2"    "FTH1"     "SH3BGRL3" "H3F3B"    "MT2A"     "H3F3A"    "APOBEC3A" "MT-CO3"   "MYL6"     "S100A9"   "SOD2"     "H1FX"     "S100A8"   "C1QA"     "BIN2"     "PLIN2"   
## [1] ""
##  [1] "FCER1A"   "CLEC10A"  "HLA-DPB1" "CD74"     "HLA-DRA"  "HLA-DRB1" "CST7"     "RPLP1"    "LMNA"     "GSN"      "IL32"     "SPINT2"   "CD7"      "GNLY"     "CCL5"     "SDC2"     "KLRB1"    "GZMB"     "NKG7"     "SMOX"     "PDLIM1"   "FGFBP2"   "TAGLN2"   "DCTN2"    "SPON2"    "GZMA"     "G0S2"     "HOPX"     "GAPDH"    "FABP5"   
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "PPBP"      "HIST1H2AC" "PF4"       "SDPR"      "NRGN"      "GNG11"     "CCL5"      "TUBB1"     "ACRBP"     "CLU"       "RGS18"     "F13A1"     "RUFY1"     "MMD"       "NGFRAP1"   "MAX"       "NCOA4"     "VCL"       "LIMS1"     "TSC22D1"   "TUBA4A"    "VIM-AS1"   "RNF11"     "YWHAH"     "MAP3K7CL"  "CCND3"     "TLN1"      "XPNPEP1"   "ETFA"      "GRAP2"    
## [1] ""
##  [1] "RPL34"         "RPLP1"         "S100A6"        "S100A4"        "LYZ"           "S100A9"        "AIF1"          "RPS19"         "S100A8"        "HLA-DRA"       "MALAT1"        "NEAT1"         "RP11-1143G9.4" "S100A12"       "HLA-DRB1"      "CD74"          "HLA-DPB1"      "CSF3R"         "OSM"           "SNAPC1"        "RAB34"         "ERO1L"         "NXT1"          "FAM101B"       "FABP5"         "RETN"          "HILPDA"        "ELL"           "FNDC3B"        "KBTBD6"       
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "GPX1"          "LYZ"           "S100A9"        "S100A8"        "S100A12"       "RP11-1143G9.4" "MIR4435-1HG"   "SMOX"          "CD9"           "GAPDH"         "SDPR"          "RGS18"         "GNG11"         "PF4"           "TUBB1"         "MPP1"          "ACTN1"         "MAP3K7CL"      "NRGN"          "ACRBP"         "RPLP1"         "TUBA1C"        "HIST1H2AC"     "PPBP"          "APP"           "C19orf59"      "RNF11"         "PLBD1"         "CLU"           "F13A1"        
## [1] ""
##  [1] "NKG7"   "GNLY"   "GZMA"   "GZMB"   "KLRB1"  "FGFBP2" "CST7"   "CD7"    "HOPX"   "SPON2"  "PRF1"   "CCL4"   "IL32"   "CMC1"   "RPS19"  "CCL5"   "MALAT1" "B2M"    "JAK1"   "MT-CO2" "BIN2"   "CD47"   "NAP1L1" "LYPD2"  "MT-CO1" "MT2A"   "CCL3"   "RAP1B"  "C1QA"   "CCND3" 
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "HLA-DPB1" "RPS19"    "NAP1L1"   "CD74"     "HLA-DRB1" "HLA-DRA"  "FTH1"     "LYPD2"    "C1QA"     "AIF1"     "VMO1"     "SAT1"     "MALAT1"   "RAP1B"    "FAM110A"  "MT2A"     "CLEC10A"  "BIN2"     "FCER1A"   "TIMP1"    "ACTB"     "ICAM2"    "SNAP23"   "NDUFA6"   "ARL6IP5"  "CD47"     "MYL6"     "SPINT2"   "CTSL"     "SNN"     
## [1] ""
##  [1] "S100A8"        "S100A9"        "S100A12"       "LYZ"           "RP11-1143G9.4" "GPX1"          "RPLP1"         "GNLY"          "S100A6"        "HOPX"          "GZMA"          "GZMB"          "KLRB1"         "SPON2"         "NKG7"          "FGFBP2"        "PRF1"          "CD7"           "CCL5"          "IL32"          "CSF3R"         "CST7"          "CCL4"          "MT-CO3"        "RETN"          "PPBP"          "RPL34"         "S100P"         "IL8"           "CYP1B1"       
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "FTL"         "FTH1"        "SAT1"        "B2M"         "AIF1"        "TMSB4X"      "PLIN2"       "S100A4"      "MALAT1"      "H3F3B"       "NEAT1"       "SH3BGRL3"    "OAZ1"        "H1FX"        "APOBEC3A"    "ERO1L"       "ACTB"        "HK2"         "NXT1"        "HILPDA"      "SRGN"        "SOD2"        "S100A6"      "RGCC"        "ADM"         "C15orf48"    "CTA-29F11.1" "SNAPC1"      "ANKRD37"     "ITM2B"      
## [1] ""
##  [1] "FCER1A"    "CLEC10A"   "HLA-DPB1"  "CD74"      "GSN"       "SPINT2"    "RPLP1"     "IL32"      "DCTN2"     "F13A1"     "CCL5"      "SDPR"      "PDLIM1"    "PPBP"      "CST7"      "HLA-DRB1"  "CCND3"     "PF4"       "DAPP1"     "YWHAH"     "GNG11"     "EGR1"      "MMD"       "GRAP2"     "NCOA4"     "TUBB1"     "TMEM70"    "MLH3"      "HIST1H2AC" "TAGLN2"   
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "HLA-DRA"     "HLA-DRB1"    "CD74"        "FCER1A"      "HLA-DPB1"    "CLEC10A"     "GAPDH"       "LYZ"         "CTA-29F11.1" "HILPDA"      "GSN"         "NXT1"        "SPINT2"      "ERO1L"       "C15orf48"    "PLIN2"       "RGCC"        "H3F3B"       "HK2"         "MAP3K8"      "SNAPC1"      "ANKRD37"     "FABP5"       "TPM4"        "ADM"         "SRGN"        "HSPA5"       "TAGLN2"      "CST7"        "RPLP1"      
## [1] ""
##  [1] "FTL"      "LYPD2"    "MT-CO2"   "RPS19"    "NEAT1"    "S100A6"   "NAP1L1"   "S100A4"   "AIF1"     "C1QA"     "SAT1"     "RAP1B"    "FAM110A"  "MT-CO1"   "RABGAP1L" "PPBP"     "VMO1"     "MT2A"     "EGR1"     "PF4"      "MARCH2"   "S100A12"  "ARRB1"    "LYL1"     "GNG11"    "ABTB1"    "OAZ1"     "MT-CO3"   "TMEM91"   "NRGN"    
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "SELPLG"   "ALOX5AP"  "GZMB"     "CTSC"     "CD68"     "FCER1G"   "SERPINF1" "CST3"     "CLIC3"    "IRF7"     "VIMP"     "TXN"      "UGCG"     "PTPRE"    "PLD4"     "S100A6"   "NPC2"     "IL3RA"    "APP"      "JKAMP"    "CD4"      "IGJ"      "PPP1R14B" "TWF2"     "TGFBI"    "SLC38A2"  "STMN1"    "MS4A6A"   "B2M"      "AMICA1"  
## [1] ""
##  [1] "RPS27"        "RPL18A"       "RPL13A"       "RPS27A"       "RPL32"        "RPL21"        "RPL13"        "RPS19"        "RPL34"        "RPS12"        "RPL41"        "CD52"         "RPS29"        "HLA-DRA"      "CD69"         "PTMA"         "RPS15A"       "LTB"          "RPL10"        "ID3"          "RPS18"        "TAGAP"        "RP5-887A10.1" "AC079767.4"   "NEIL1"        "YBX3"         "ZNF331"       "RHOB"         "IGLL5"        "HLA-DRB1"    
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "CASP2"      "IL32"       "ITM2A"      "PHTF2"      "NUAK2"      "SKAP1"      "RABEP2"     "MRPS2"      "TMEM80"     "MT2A"       "ZNF83"      "RAB6A"      "COQ10B"     "PTPN4"      "SDR39U1"    "FBXO3"      "ANXA1"      "IFI6"       "DCP2"       "STK4"       "ITGB7"      "PHF6"       "AC016831.7" "CCDC130"    "LMNA"       "MECP2"      "GNG2"       "COPS8"      "TRAPPC2"    "EML4"      
## [1] ""
##  [1] "GZMB"     "SERPINF1" "FCER1G"   "CLIC3"    "CST3"     "IRF7"     "NPC2"     "UGCG"     "VIMP"     "APP"      "PLD4"     "PTPRE"    "CD4"      "IL3RA"    "PPP1R14B" "ALOX5AP"  "TXN"      "MS4A6A"   "AMICA1"   "TGFBI"    "FCER1A"   "HIGD1A"   "PTGDS"    "CCDC50"   "STMN1"    "RNASE6"   "IGJ"      "RRBP1"    "XBP1"     "SAMHD1"  
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "TMSB10"   "CD52"     "TMSB4X"   "ACTB"     "ACTG1"    "IGLL5"    "MZB1"     "LTB"      "SUB1"     "PPIB"     "SDF2L1"   "MT-CO2"   "C19orf10" "ITGB1"    "SEC11C"   "IGJ"      "B2M"      "SSR3"     "ANXA6"    "HLA-C"    "HLA-A"    "MT-CO1"   "CALR"     "MT-CYB"   "ITGB7"    "DNPH1"    "PDIA6"    "MT-ND4"   "TXN"      "MRPS14"  
## [1] ""
##  [1] "MALAT1" "FTH1"   "RPS27"  "RPL21"  "EIF1"   "H3F3B"  "RPL34"  "PMAIP1" "RPS27A" "ZNF331" "RGS2"   "SNX9"   "RPL32"  "TRAF4"  "RPS29"  "EEF1A1" "RGS1"   "PTMA"   "IDI1"   "NEAT1"  "LY9"    "PIK3R1" "BBC3"   "WSB1"   "NR4A2"  "RPS19"  "PTGDS"  "PIM3"   "CD69"   "H1FX"  
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "CD74"     "HLA-DRA"  "LTB"      "HLA-DRB1" "TMSB4X"   "CD52"     "RPS27"    "RPL41"    "IL4R"     "SNX10"    "RNASE6"   "ACTB"     "TMSB10"   "CD72"     "PLD4"     "RPL34"    "ALOX5AP"  "TMEM80"   "CD4"      "SELPLG"   "RPL13A"   "CELF2"    "SCOC"     "ZCCHC7"   "AMICA1"   "RPL21"    "ELMO1"    "FCER1A"   "TGFBI"    "SDAD1"   
## [1] ""
##  [1] "SDF2L1"   "SEC11C"   "PPIB"     "C19orf10" "MZB1"     "XBP1"     "PDIA6"    "SSR3"     "IGJ"      "SUB1"     "NEAT1"    "PTMA"     "ZNF331"   "LITAF"    "NR4A2"    "RGS2"     "CALR"     "DERL1"    "FTH1"     "RPLP1"    "ITGB1"    "H3F3B"    "LY9"      "IDI1"     "RGS1"     "EIF1"     "BBC3"     "SLC2A3"   "CORO7"    "RPS15A"  
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "RPLP1"    "RPL13"    "RPS12"    "RPL32"    "RPL10"    "RPS18"    "RPS19"    "RPS15A"   "EEF1A1"   "MGAT4A"   "IGJ"      "EBPL"     "RPL41"    "USP22"    "RPL21"    "PTGDS"    "PIK3R1"   "SUMF2"    "ITM2A"    "PPP1CC"   "MARK3"    "GMCL1"    "ACAP2"    "SSR3"     "SDF2L1"   "PRKAG1"   "MRPS10"   "ITGB1BP1" "PPP1R14B" "ACAA1"   
## [1] ""
##  [1] "HLA-DRB1" "CD74"     "FOS"      "HLA-DRA"  "LITAF"    "H3F3B"    "MALAT1"   "MT-CO1"   "HEXIM1"   "MT-CO3"   "RGS1"     "PTMA"     "CD69"     "LYZ"      "RGS2"     "TTC14"    "NEAT1"    "IDI1"     "FTH1"     "HSPB1"    "ZNF331"   "EIF1"     "MT-CO2"   "MT-CYB"   "CD2BP2"   "MT-ND4"   "NCOA3"    "SAMHD1"   "PRPF4B"   "CD72"    
## [1] ""
## [1] ""

## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
## [1] "PC1"
##  [1] "SELPLG"   "GZMB"     "ALOX5AP"  "CTSC"     "CD68"     "FCER1G"   "SERPINF1" "CST3"     "CLIC3"    "IRF7"     "VIMP"     "TXN"      "UGCG"     "PTPRE"    "NPC2"     "PLD4"     "IL3RA"    "S100A6"   "APP"      "CD4"      "JKAMP"    "PPP1R14B" "IGJ"      "TGFBI"    "TWF2"     "SLC38A2"  "STMN1"    "MS4A6A"   "AMICA1"   "HIGD1A"  
## [1] ""
##  [1] "RPS27"        "CD52"         "RPL18A"       "RPL13A"       "RPL32"        "RPS27A"       "RPL21"        "RPL13"        "LTB"          "RPS19"        "RPL34"        "RPS12"        "RPL41"        "RPS29"        "HLA-DRA"      "CD69"         "RPS15A"       "IGLL5"        "RPL10"        "CD72"         "ID3"          "RPS18"        "RP5-887A10.1" "TAGAP"        "AC079767.4"   "PTMA"         "NEIL1"        "YBX3"         "ANXA6"        "RHOB"        
## [1] ""
## [1] ""
## [1] "PC2"
##  [1] "GZMB"     "SERPINF1" "FCER1G"   "CLIC3"    "CST3"     "IRF7"     "NPC2"     "UGCG"     "VIMP"     "APP"      "PLD4"     "PTPRE"    "CD4"      "IL3RA"    "PPP1R14B" "ALOX5AP"  "TXN"      "MS4A6A"   "AMICA1"   "TGFBI"    "FCER1A"   "PTGDS"    "HIGD1A"   "CCDC50"   "STMN1"    "RNASE6"   "IGJ"      "RRBP1"    "XBP1"     "SAMHD1"  
## [1] ""
##  [1] "CD52"       "CASP2"      "IL32"       "ITM2A"      "PHTF2"      "NUAK2"      "RABEP2"     "SKAP1"      "TMEM80"     "MRPS2"      "MT2A"       "ZNF83"      "RAB6A"      "COQ10B"     "PTPN4"      "SDR39U1"    "FBXO3"      "ANXA1"      "IFI6"       "ITGB7"      "DCP2"       "STK4"       "PHF6"       "AC016831.7" "TRAPPC2"    "LMNA"       "DNPH1"      "COPS8"      "CCDC130"    "MECP2"     
## [1] ""
## [1] ""
## [1] "PC3"
##  [1] "RPS27"   "RPL21"   "RPL34"   "MALAT1"  "RPL32"   "CD74"    "RPS27A"  "RPS29"   "RPL13"   "HLA-DRA" "LTB"     "RPS19"   "NPC2"    "EEF1A1"  "UGCG"    "RNASE6"  "SIDT1"   "PTGDS"   "RPL18A"  "APP"     "ALOX5AP" "RPL13A"  "GZMB"    "TRAF4"   "APPL1"   "CD68"    "MGAT4A"  "PLD4"    "SFPQ"    "H1FX"   
## [1] ""
##  [1] "MZB1"     "SDF2L1"   "C19orf10" "PPIB"     "SEC11C"   "SUB1"     "SSR3"     "IGJ"      "ACTG1"    "ITGB1"    "CALR"     "PDIA6"    "MT-CO2"   "XBP1"     "HLA-A"    "IGLL5"    "DERL1"    "HLA-C"    "ITGB7"    "MT-CO1"   "MT-CYB"   "MRPS14"   "TXN"      "S100A6"   "MT-CO3"   "MT-ND4"   "B2M"      "TMSB10"   "LITAF"    "CD2BP2"  
## [1] ""
## [1] ""
## [1] "PC4"
##  [1] "CD74"          "HLA-DRB1"      "HLA-DRA"       "MALAT1"        "FOS"           "H3F3B"         "MT-CO1"        "LITAF"         "TMSB4X"        "PTMA"          "HEXIM1"        "MT-CO3"        "TTC14"         "LYZ"           "MT-CO2"        "FTH1"          "EIF1"          "ACTB"          "ZNF331"        "ZCCHC7"        "SAMHD1"        "MT-ND4"        "CD72"          "HSPB1"         "MT-CYB"        "NEAT1"         "CD69"          "RGS1"          "RP11-1143G9.4" "NCOA3"        
## [1] ""
##  [1] "RPLP1"    "RPS12"    "RPL10"    "RPS15A"   "RPL32"    "RPL13"    "RPS18"    "MGAT4A"   "RPS19"    "EEF1A1"   "IGJ"      "USP22"    "SDF2L1"   "PIK3R1"   "SSR3"     "PTGDS"    "EBPL"     "ITM2A"    "RPL21"    "GMCL1"    "SUMF2"    "RPS27A"   "MARK3"    "CORO7"    "IRF4"     "PDIA6"    "XBP1"     "IL32"     "PPP1R14B" "ACAP2"   
## [1] ""
## [1] ""
## [1] "PC5"
##  [1] "MGAT4A"    "IRF4"      "VHL"       "ADAM17"    "NKG7"      "GNB1"      "CCDC14"    "RICTOR"    "PDIA6"     "RAB11FIP1" "H2AFJ"     "MT-ND2"    "CCDC69"    "THAP7"     "RAP2C"     "YIPF5"     "TLE4"      "SIDT1"     "HPS4"      "TRAF4"     "STMN1"     "H3F3B"     "MT-CYB"    "SDAD1"     "MT-CO3"    "DSTN"      "TRAPPC2"   "MT-CO1"    "MT-ND4"    "RPS27A"   
## [1] ""
##  [1] "HLA-DRA"  "SELPLG"   "IL3RA"    "AMICA1"   "MS4A6A"   "CD68"     "FCER1A"   "CD4"      "CTSC"     "FCER1G"   "SCOC"     "HLA-DRB1" "TGFBI"    "IRF7"     "S100A6"   "SAMHD1"   "LST1"     "TP53I13"  "SMAP1"    "MRPS2"    "PRKAG1"   "RAB22A"   "TWF2"     "ACTG1"    "JKAMP"    "ITGB1BP1" "PPIE"     "TXN"      "CD74"     "DCP2"    
## [1] ""
## [1] ""

df <- map(c("not regressed", "regressed"), function(regr) {
  tsne_list %>% 
    map(regr) %>% 
    map("data") %>% 
    bind_rows(.id = "cell_type")
})
names(df) <- c("original", "regressed")
df <- bind_rows(df, .id = "is_regressed")

tsne_regressed <- df %>% 
  mutate(cell_type = factor(cell_type, cell_types)) %>% 
  ggplot(aes_string("tSNE_1", "tSNE_2", color = "ident")) +
  geom_point(size = 0.6) +
  facet_grid(is_regressed ~ cell_type) +
  labs(x = "tSNE1", y = "tSNE2") +
  scale_color_manual("", values = c("red2", "royalblue1")) +
  theme_classic() +
  guides(colour = guide_legend(override.aes = list(size = 4)))
tsne_regressed

ggsave(
  filename = str_c("results/plots/", Sys.Date(), "_tsne_regressed.pdf"),
  plot = tsne_regressed,
  device = "pdf",
  width = 12,
  height = 7
)
saveRDS(tsne_regressed, file = "results/R_objects/tsne_regressed_gg.rds")

# Plot only CD4
tsne_regressed_cd4 <- df %>% 
  dplyr::filter(cell_type == "CD4 T") %>% 
  ggplot(aes(tSNE_1, tSNE_2, color = ident)) +
    geom_point(size = 0.25) +
    facet_grid(is_regressed ~ .) +
    theme_classic2() +
    labs(x = "tSNE1", y = "tSNE2") +
    scale_color_manual("", values = c("red2", "royalblue1")) 
saveRDS(tsne_regressed_cd4, file = "results/R_objects/tsne_regressed_cd4.rds")

2 Supplementary figure

plot_list <- readRDS("results/R_objects/validation_plots.rds")
plot_list[[4]] <- tsne_regressed
tsne_regressed +  
    theme(legend.position = "none", 
          strip.background = element_rect(fill = NA))
plot_list <- map(plot_list, function(gg) {
  gg + 
    theme(legend.position = "none", 
          strip.background = element_rect(fill = "white"))
})
metasign_valid_gg <- ggarrange(
  plotlist = plot_list[1:3], 
  ncol = 1, 
  nrow = 3, 
  labels = "auto", 
  align = "v"
)
metasign_valid_gg2 <- ggarrange(
  plotlist = list(metasign_valid_gg, plot_list[[4]]), 
  ncol = 1, 
  nrow = 2, 
  heights = c(0.75, 0.25),
  labels = c("", "d")
)
ggsave(
  filename = str_c("doc/figures/R/", date, "_validation_figure.pdf"), 
  plot = metasign_valid_gg2, 
  width = 19, 
  height = 27,
  units = "cm"
)
metasign_valid_gg

3 Session Info

sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] forcats_0.4.0               stringr_1.4.0               dplyr_0.8.0.1               readr_1.3.1                 tidyr_0.8.3                 tibble_2.1.1                tidyverse_1.2.1             ggridges_0.5.1              scales_1.0.0                ggplotify_0.0.3             VennDiagram_1.6.20          futile.logger_1.4.3         GOstats_2.48.0              graph_1.60.0                Category_2.48.1             ROCR_1.0-7                  gplots_3.0.1.1              caret_6.0-82                lattice_0.20-38             plotROC_2.2.1               ggrepel_0.8.0               purrr_0.3.2                 pheatmap_1.0.12             SC3_1.10.1                  biomaRt_2.38.0              org.Hs.eg.db_3.7.0          ggpubr_0.2                  magrittr_1.5                EnsDb.Hsapiens.v86_2.99.0   ensembldb_2.6.7             AnnotationFilter_1.6.0      GenomicFeatures_1.34.7      AnnotationDbi_1.44.0        Seurat_2.3.4                Matrix_1.2-17               cowplot_0.9.4               scran_1.10.2                scater_1.10.1               ggplot2_3.1.0               SingleCellExperiment_1.4.1  SummarizedExperiment_1.12.0 DelayedArray_0.8.0         
## [43] BiocParallel_1.16.6         matrixStats_0.54.0          Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.2         IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0         BiocStyle_2.10.0           
## 
## loaded via a namespace (and not attached):
##   [1] rtracklayer_1.42.2       AnnotationForge_1.24.0   ModelMetrics_1.2.2       prabclus_2.2-7           R.methodsS3_1.7.1        pkgmaker_0.27            acepack_1.4.1            bit64_0.9-7              knitr_1.22               irlba_2.3.3              R.utils_2.8.0            data.table_1.12.0        rpart_4.1-13             RCurl_1.95-4.12          doParallel_1.0.14        generics_0.0.2           metap_1.1                snow_0.4-3               lambda.r_1.2.3           RSQLite_2.1.1            RANN_2.6.1               proxy_0.4-23             bit_1.1-14               xml2_1.2.0               lubridate_1.7.4          httpuv_1.5.0             assertthat_0.2.1         viridis_0.5.1            gower_0.2.0              xfun_0.5                 hms_0.4.2                evaluate_0.13            promises_1.0.1           DEoptimR_1.0-8           progress_1.2.0           readxl_1.3.1             caTools_1.17.1.2         Rgraphviz_2.26.0         igraph_1.2.4             DBI_1.0.0                htmlwidgets_1.3          backports_1.1.3          bookdown_0.9             trimcluster_0.1-2.1      annotate_1.60.1          gbRd_0.4-11              withr_2.1.2             
##  [48] robustbase_0.93-4        checkmate_1.9.1          GenomicAlignments_1.18.1 prettyunits_1.0.2        mclust_5.4.3             cluster_2.0.7-1          ape_5.3                  segmented_0.5-3.0        lazyeval_0.2.2           crayon_1.3.4             genefilter_1.64.0        hdf5r_1.0.1              labeling_0.3             edgeR_3.24.3             recipes_0.1.5            pkgconfig_2.0.2          nlme_3.1-137             vipor_0.4.5              ProtGenerics_1.14.0      nnet_7.3-12              rlang_0.3.3              diptest_0.75-7           registry_0.5-1           modelr_0.1.4             doSNOW_1.0.16            cellranger_1.1.0         lmtest_0.9-36            rngtools_1.3.1           Rhdf5lib_1.4.3           zoo_1.8-5                base64enc_0.1-3          beeswarm_0.2.3           png_0.1-7                viridisLite_0.3.0        bitops_1.0-6             R.oo_1.22.0              KernSmooth_2.23-15       Biostrings_2.50.2        blob_1.1.1               DelayedMatrixStats_1.4.0 doRNG_1.7.1              lars_1.2                 gridGraphics_0.3-0       GSEABase_1.44.0          memoise_1.1.0            plyr_1.8.4               ica_1.0-2               
##  [95] bibtex_0.4.2             gdata_2.18.0             zlibbioc_1.28.0          compiler_3.5.1           lsei_1.2-0               RColorBrewer_1.1-2       rrcov_1.4-7              fitdistrplus_1.0-14      cli_1.1.0                Rsamtools_1.34.1         dtw_1.20-1               XVector_0.22.0           pbapply_1.4-0            formatR_1.6              htmlTable_1.13.1         Formula_1.2-3            MASS_7.3-51.3            tidyselect_0.2.5         stringi_1.4.3            yaml_2.2.0               locfit_1.5-9.1           latticeExtra_0.6-28      tools_3.5.1              rstudioapi_0.10          foreach_1.4.4            foreign_0.8-71           gridExtra_2.3            prodlim_2018.04.18       Rtsne_0.15               rvcheck_0.1.3            digest_0.6.18            BiocManager_1.30.4       lava_1.6.5               shiny_1.2.0              fpc_2.1-11.1             Rcpp_1.0.1               broom_0.5.1              SDMTools_1.1-221         later_0.8.0              WriteXLS_4.1.0           httr_1.4.0               npsurv_0.4-0             kernlab_0.9-27           Rdpack_0.10-1            colorspace_1.4-1         rvest_0.3.2              XML_3.98-1.19           
## [142] reticulate_1.11.1        splines_3.5.1            RBGL_1.58.2              statmod_1.4.30           flexmix_2.3-15           xtable_1.8-3             futile.options_1.0.1     jsonlite_1.6             dynamicTreeCut_1.63-1    timeDate_3043.102        modeltools_0.2-22        ipred_0.9-8              R6_2.4.0                 Hmisc_4.2-0              pillar_1.3.1             htmltools_0.3.6          mime_0.6                 glue_1.3.1               BiocNeighbors_1.0.0      class_7.3-15             codetools_0.2-16         tsne_0.1-3               pcaPP_1.9-73             mvtnorm_1.0-10           mixtools_1.1.0           curl_3.3                 ggbeeswarm_0.6.0         gtools_3.8.1             GO.db_3.7.0              survival_2.44-1.1        limma_3.38.3             rmarkdown_1.12           munsell_0.5.0            e1071_1.7-1              rhdf5_2.26.2             GenomeInfoDbData_1.2.0   iterators_1.0.10         HDF5Array_1.10.1         haven_2.1.0              reshape2_1.4.3           gtable_0.3.0